Essay 1 - Culture media growth fitness
- 1 Exploratory data analysis
- 2 Comprobatory data analysis
1 Exploratory data analysis
1.1 Get raw data
1.2 Plot data profile
1.3 Remove Control from raw dataset
1.4 Plot observed data as a scatterplot
1.5 Clear dataset
Remove values with sd close to zero.
1.6 Plot observed data as a scatterplot
2 Comprobatory data analysis
2.1 Test if essay have some effect on essay
## Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
## Formula: average ~ day:code:inocPosByClone + (1 | essay)
## Data: dataset_clean
##
## REML criterion at convergence: 14728.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.5418 -0.4878 0.0130 0.4983 5.8274
##
## Random effects:
## Groups Name Variance Std.Dev.
## essay (Intercept) 223.7 14.96
## Residual 181.6 13.48
## Number of obs: 1850, groups: essay, 2
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -1.1659 10.6022 1.0078 -0.110 0.930165
## day:codeP. palmivora | 1102:inocPosByCloneCCN51 | A 13.5564 0.7686 1784.0004 17.639 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCCN51 | A 14.2398 0.8377 1784.0053 16.999 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCCN51 | A 10.8872 1.0741 1784.0385 10.136 < 2e-16 ***
## day:codeP. palmivora | 920:inocPosByCloneCCN51 | A 9.5624 0.8377 1784.0053 11.415 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCCN51 | A 20.1468 0.7156 1784.0006 28.154 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCCN51 | A 17.8950 0.7156 1784.0006 25.007 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCCN51 | A 15.0331 0.7686 1784.0004 19.560 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCCN51 | A 16.1768 0.7686 1784.0004 21.048 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCCN51 | B 15.1860 0.8377 1784.0053 18.128 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCCN51 | B 14.0754 0.7156 1784.0006 19.670 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCCN51 | B 3.8328 1.0682 1784.0002 3.588 0.000342 ***
## day:codeP. palmivora | 920:inocPosByCloneCCN51 | B 9.0415 0.8371 1784.0001 10.801 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCCN51 | B 19.6417 0.7686 1784.0004 25.557 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCCN51 | B 18.6281 0.7686 1784.0004 24.238 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCCN51 | B 15.8744 0.7156 1784.0006 22.184 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCCN51 | B 18.8428 0.7156 1784.0006 26.332 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCepec_2004 | A 12.2822 0.8377 1784.0053 14.662 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCepec_2004 | A 13.2649 0.9330 1784.0190 14.217 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCepec_2004 | A 4.9820 1.8318 1784.0133 2.720 0.006598 **
## day:codeP. palmivora | 920:inocPosByCloneCepec_2004 | A 4.4176 0.7686 1784.0004 5.748 1.06e-08 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCepec_2004 | A 15.7829 0.8377 1784.0053 18.841 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCepec_2004 | A 19.4419 0.7156 1784.0006 27.169 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCepec_2004 | A 19.4731 0.7156 1784.0006 27.213 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCepec_2004 | A 18.3339 0.7156 1784.0006 25.621 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCepec_2004 | B 12.3770 0.7686 1784.0004 16.104 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCepec_2004 | B 12.9607 0.7686 1784.0004 16.864 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCepec_2004 | B 13.5790 1.8318 1784.0133 7.413 1.90e-13 ***
## day:codeP. palmivora | 920:inocPosByCloneCepec_2004 | B 8.8235 0.8377 1784.0053 10.533 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCepec_2004 | B 16.8578 0.7686 1784.0004 21.934 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCepec_2004 | B 18.5066 0.7156 1784.0006 25.862 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCepec_2004 | B 15.4703 0.7156 1784.0006 21.619 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCepec_2004 | B 17.9525 0.7686 1784.0004 23.359 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCP49 | A 13.9143 0.7686 1784.0004 18.104 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCP49 | A 13.9541 0.7156 1784.0006 19.500 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCP49 | A 4.2489 0.8380 1784.0081 5.070 4.39e-07 ***
## day:codeP. palmivora | 920:inocPosByCloneCP49 | A 6.6549 0.9308 1784.0022 7.150 1.26e-12 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCP49 | A 19.8004 0.7156 1784.0006 27.670 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCP49 | A 18.0389 0.7156 1784.0006 25.209 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCP49 | A 17.1462 0.7156 1784.0006 23.961 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCP49 | A 18.7911 0.7156 1784.0006 26.260 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCP49 | B 13.5646 0.7156 1784.0006 18.956 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCP49 | B 11.4188 0.7156 1784.0006 15.957 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCP49 | B 2.9362 1.0682 1784.0002 2.749 0.006045 **
## day:codeP. palmivora | 920:inocPosByCloneCP49 | B 5.8241 0.9330 1784.0190 6.242 5.38e-10 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCP49 | B 22.3973 0.7156 1784.0006 31.299 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCP49 | B 17.7299 0.7156 1784.0006 24.777 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCP49 | B 20.5629 0.7686 1784.0004 26.755 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCP49 | B 17.0820 0.7156 1784.0006 23.871 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByClonePS1319 | A 12.2811 0.7686 1784.0004 15.979 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByClonePS1319 | A 13.2676 0.7156 1784.0006 18.541 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByClonePS1319 | A 7.8100 1.0695 1784.0084 7.303 4.23e-13 ***
## day:codeP. palmivora | 920:inocPosByClonePS1319 | A 8.6606 0.9330 1784.0190 9.282 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByClonePS1319 | A 18.0995 0.7156 1784.0006 25.293 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByClonePS1319 | A 17.6890 0.7156 1784.0006 24.720 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByClonePS1319 | A 19.6421 0.7156 1784.0006 27.449 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByClonePS1319 | A 15.3929 0.7686 1784.0004 20.028 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByClonePS1319 | B 13.9583 0.8377 1784.0053 16.663 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByClonePS1319 | B 11.9219 0.7156 1784.0006 16.660 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByClonePS1319 | B 2.7071 1.3008 1784.0010 2.081 0.037561 *
## day:codeP. palmivora | 920:inocPosByClonePS1319 | B 5.8007 0.7686 1784.0004 7.548 7.03e-14 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByClonePS1319 | B 20.5787 0.7156 1784.0006 28.758 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByClonePS1319 | B 16.5238 0.7156 1784.0006 23.091 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByClonePS1319 | B 16.2955 0.7156 1784.0006 22.772 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByClonePS1319 | B 17.9557 0.7156 1784.0006 25.092 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 65 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it2.1.1 How much the essay is important to explain about the total variance?
## [1] "Variance: 55.1895378682 %"2.2 Test if replicate have some effect on essay
## Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
## Formula: average ~ day:code:inocPosByClone + (1 | replicate)
## Data: dataset_clean
##
## REML criterion at convergence: 15469.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.3076 -0.5044 0.1467 0.6544 3.9949
##
## Random effects:
## Groups Name Variance Std.Dev.
## replicate (Intercept) 18.93 4.351
## Residual 274.51 16.568
## Number of obs: 1850, groups: replicate, 4
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.2749 2.3580 3.7770 0.965 0.392288
## day:codeP. palmivora | 1102:inocPosByCloneCCN51 | A 13.7565 0.9452 1782.0232 14.554 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCCN51 | A 15.1689 1.0296 1782.0591 14.732 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCCN51 | A 7.6447 1.3139 1782.1089 5.818 7.03e-09 ***
## day:codeP. palmivora | 920:inocPosByCloneCCN51 | A 10.4881 1.0296 1782.0529 10.186 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCCN51 | A 19.8684 0.8796 1781.9284 22.587 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCCN51 | A 17.6165 0.8796 1781.9284 20.027 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCCN51 | A 15.2332 0.9452 1782.0232 16.117 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCCN51 | A 16.3741 0.9452 1782.0190 17.324 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCCN51 | B 16.1151 1.0296 1782.0591 15.651 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCCN51 | B 13.7970 0.8796 1781.9284 15.685 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCCN51 | B 4.4343 1.3139 1782.1089 3.375 0.000754 ***
## day:codeP. palmivora | 920:inocPosByCloneCCN51 | B 9.2367 1.0305 1782.3210 8.963 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCCN51 | B 19.8910 0.9451 1782.0058 21.046 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCCN51 | B 18.8254 0.9452 1782.0190 19.917 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCCN51 | B 15.5959 0.8796 1781.9284 17.730 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCCN51 | B 18.5644 0.8796 1781.9284 21.105 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCepec_2004 | A 13.2113 1.0296 1782.0591 12.831 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCepec_2004 | A 15.2096 1.1443 1782.0394 13.292 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCepec_2004 | A 1.8319 2.2537 1782.4790 0.813 0.416414
## day:codeP. palmivora | 920:inocPosByCloneCepec_2004 | A 4.6668 0.9451 1782.0058 4.938 8.64e-07 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCepec_2004 | A 16.6497 1.0297 1782.0784 16.169 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCepec_2004 | A 19.1635 0.8796 1781.9284 21.786 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCepec_2004 | A 19.1947 0.8796 1781.9284 21.822 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCepec_2004 | A 18.0555 0.8796 1781.9284 20.526 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCepec_2004 | B 12.6262 0.9451 1782.0058 13.360 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCepec_2004 | B 13.1581 0.9452 1782.0190 13.921 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCepec_2004 | B 10.4289 2.2537 1782.4790 4.628 3.97e-06 ***
## day:codeP. palmivora | 920:inocPosByCloneCepec_2004 | B 9.7526 1.0296 1782.0591 9.472 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCepec_2004 | B 17.1070 0.9451 1782.0058 18.101 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCepec_2004 | B 18.2282 0.8796 1781.9284 20.723 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCepec_2004 | B 15.1919 0.8796 1781.9284 17.271 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCepec_2004 | B 18.1527 0.9452 1782.0232 19.205 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCP49 | A 14.1116 0.9452 1782.0190 14.930 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCP49 | A 13.6757 0.8796 1781.9284 15.547 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCP49 | A 3.3532 1.0304 1782.3060 3.254 0.001158 **
## day:codeP. palmivora | 920:inocPosByCloneCP49 | A 7.1622 1.1464 1782.4021 6.248 5.20e-10 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCP49 | A 19.5219 0.8796 1781.9284 22.194 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCP49 | A 17.7605 0.8796 1781.9284 20.191 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCP49 | A 16.8678 0.8796 1781.9284 19.176 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCP49 | A 18.5127 0.8796 1781.9284 21.046 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCP49 | B 13.2861 0.8796 1781.9284 15.104 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCP49 | B 11.1404 0.8796 1781.9284 12.665 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCP49 | B 3.6358 1.3171 1782.5767 2.761 0.005829 **
## day:codeP. palmivora | 920:inocPosByCloneCP49 | B 7.7687 1.1443 1782.0394 6.789 1.53e-11 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCP49 | B 22.1189 0.8796 1781.9284 25.146 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCP49 | B 17.4514 0.8796 1781.9284 19.840 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCP49 | B 20.7602 0.9452 1782.0190 21.965 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCP49 | B 16.8036 0.8796 1781.9284 19.103 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByClonePS1319 | A 12.4784 0.9452 1782.0190 13.202 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByClonePS1319 | A 12.9891 0.8796 1781.9284 14.767 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByClonePS1319 | A 6.5933 1.3171 1782.5771 5.006 6.11e-07 ***
## day:codeP. palmivora | 920:inocPosByClonePS1319 | A 10.6053 1.1443 1782.0394 9.268 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByClonePS1319 | A 17.8211 0.8796 1781.9284 20.260 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByClonePS1319 | A 17.4106 0.8796 1781.9284 19.793 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByClonePS1319 | A 19.3636 0.8796 1781.9284 22.014 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByClonePS1319 | A 15.5903 0.9452 1782.0190 16.495 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByClonePS1319 | B 14.8251 1.0297 1782.0784 14.397 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByClonePS1319 | B 11.6434 0.8796 1781.9284 13.237 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByClonePS1319 | B 2.4486 1.6014 1782.2957 1.529 0.126426
## day:codeP. palmivora | 920:inocPosByClonePS1319 | B 6.0009 0.9452 1782.0232 6.349 2.74e-10 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByClonePS1319 | B 20.3003 0.8796 1781.9284 23.078 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByClonePS1319 | B 16.2454 0.8796 1781.9284 18.469 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByClonePS1319 | B 16.0171 0.8796 1781.9284 18.209 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByClonePS1319 | B 17.6773 0.8796 1781.9284 20.096 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 65 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it2.2.1 How much the replicate is important to explain about the total variance?
## [1] "Variance: 6.4506951189 %"2.3 Generate full model
## boundary (singular) fit: see ?isSingular## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's method ['lmerModLmerTest']
## Formula: average ~ day:code:inocPosByClone + (1 | day:code:inocPosByClone)
## Data: dataset_clean
##
## AIC BIC logLik deviance df.resid
## 15771.8 16141.8 -7818.9 15637.8 1783
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.4004 -0.5033 0.1981 0.6475 3.9646
##
## Random effects:
## Groups Name Variance Std.Dev.
## day:code:inocPosByClone (Intercept) 0.0 0.00
## Residual 274.5 16.57
## Number of obs: 1850, groups: day:code:inocPosByClone, 320
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.4054 0.9034 1850.0000 1.556 0.11994
## day:codeP. palmivora | 1102:inocPosByCloneCCN51 | A 13.8161 0.9447 1850.0000 14.624 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCCN51 | A 15.2684 1.0290 1850.0000 14.838 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCCN51 | A 7.3029 1.3132 1850.0000 5.561 3.07e-08 ***
## day:codeP. palmivora | 920:inocPosByCloneCCN51 | A 10.5910 1.0290 1850.0000 10.292 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCCN51 | A 19.8574 0.8796 1850.0000 22.575 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCCN51 | A 17.6055 0.8796 1850.0000 20.015 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCCN51 | A 15.2928 0.9447 1850.0000 16.187 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCCN51 | A 16.4365 0.9447 1850.0000 17.398 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCCN51 | B 16.2146 1.0290 1850.0000 15.757 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCCN51 | B 13.7860 0.8796 1850.0000 15.673 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCCN51 | B 4.0925 1.3132 1850.0000 3.117 0.00186 **
## day:codeP. palmivora | 920:inocPosByCloneCCN51 | B 8.9168 1.0290 1850.0000 8.665 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCCN51 | B 19.9015 0.9447 1850.0000 21.065 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCCN51 | B 18.8878 0.9447 1850.0000 19.992 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCCN51 | B 15.5849 0.8796 1850.0000 17.718 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCCN51 | B 18.5534 0.8796 1850.0000 21.093 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCepec_2004 | A 13.3107 1.0290 1850.0000 12.935 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCepec_2004 | A 15.4467 1.1439 1850.0000 13.504 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCepec_2004 | A 1.3976 2.2476 1850.0000 0.622 0.53414
## day:codeP. palmivora | 920:inocPosByCloneCepec_2004 | A 4.6773 0.9447 1850.0000 4.951 8.06e-07 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCepec_2004 | A 16.8115 1.0290 1850.0000 16.337 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCepec_2004 | A 19.1525 0.8796 1850.0000 21.774 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCepec_2004 | A 19.1837 0.8796 1850.0000 21.809 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCepec_2004 | A 18.0445 0.8796 1850.0000 20.514 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCepec_2004 | B 12.6367 0.9447 1850.0000 13.376 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCepec_2004 | B 13.2205 0.9447 1850.0000 13.994 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCepec_2004 | B 9.9946 2.2476 1850.0000 4.447 9.24e-06 ***
## day:codeP. palmivora | 920:inocPosByCloneCepec_2004 | B 9.8521 1.0290 1850.0000 9.574 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCepec_2004 | B 17.1175 0.9447 1850.0000 18.119 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCepec_2004 | B 18.2172 0.8796 1850.0000 20.711 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCepec_2004 | B 15.1809 0.8796 1850.0000 17.259 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCepec_2004 | B 18.2122 0.9447 1850.0000 19.277 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCP49 | A 14.1740 0.9447 1850.0000 15.003 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCP49 | A 13.6647 0.8796 1850.0000 15.535 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCP49 | A 2.9710 1.0290 1850.0000 2.887 0.00393 **
## day:codeP. palmivora | 920:inocPosByCloneCP49 | A 7.3951 1.1439 1850.0000 6.465 1.29e-10 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCP49 | A 19.5109 0.8796 1850.0000 22.181 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCP49 | A 17.7495 0.8796 1850.0000 20.179 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCP49 | A 16.8568 0.8796 1850.0000 19.164 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCP49 | A 18.5017 0.8796 1850.0000 21.034 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByCloneCP49 | B 13.2752 0.8796 1850.0000 15.092 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByCloneCP49 | B 11.1294 0.8796 1850.0000 12.653 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByCloneCP49 | B 3.1959 1.3132 1850.0000 2.434 0.01504 *
## day:codeP. palmivora | 920:inocPosByCloneCP49 | B 8.0059 1.1439 1850.0000 6.999 3.60e-12 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByCloneCP49 | B 22.1079 0.8796 1850.0000 25.134 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByCloneCP49 | B 17.4405 0.8796 1850.0000 19.827 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByCloneCP49 | B 20.8226 0.9447 1850.0000 22.040 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByCloneCP49 | B 16.7926 0.8796 1850.0000 19.091 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByClonePS1319 | A 12.5408 0.9447 1850.0000 13.274 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByClonePS1319 | A 12.9782 0.8796 1850.0000 14.754 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByClonePS1319 | A 6.1477 1.3132 1850.0000 4.682 3.05e-06 ***
## day:codeP. palmivora | 920:inocPosByClonePS1319 | A 10.8424 1.1439 1850.0000 9.479 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByClonePS1319 | A 17.8101 0.8796 1850.0000 20.248 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByClonePS1319 | A 17.3996 0.8796 1850.0000 19.781 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByClonePS1319 | A 19.3526 0.8796 1850.0000 22.001 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByClonePS1319 | A 15.6527 0.9447 1850.0000 16.568 < 2e-16 ***
## day:codeP. palmivora | 1102:inocPosByClonePS1319 | B 14.9869 1.0290 1850.0000 14.564 < 2e-16 ***
## day:codeP. palmivora | 1158:inocPosByClonePS1319 | B 11.6325 0.8796 1850.0000 13.225 < 2e-16 ***
## day:codeP. palmivora | 906:inocPosByClonePS1319 | B 2.0058 1.5988 1850.0000 1.255 0.20979
## day:codeP. palmivora | 920:inocPosByClonePS1319 | B 6.0605 0.9447 1850.0000 6.415 1.78e-10 ***
## day:codeP. theobromicola sp. nov. | 1091:inocPosByClonePS1319 | B 20.2893 0.8796 1850.0000 23.066 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:inocPosByClonePS1319 | B 16.2344 0.8796 1850.0000 18.456 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:inocPosByClonePS1319 | B 16.0061 0.8796 1850.0000 18.197 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:inocPosByClonePS1319 | B 17.6663 0.8796 1850.0000 20.084 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 65 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## convergence code: 0
## boundary (singular) fit: see ?isSingular2.3.1 Plot final model adjust
2.3.2 Test significance of fixed effects
2.3.3 Test significance of random effects
2.3.4 Plot a residual histogram
2.3.5 Plot observed vs predicted data as a scatterplot
2.4 Perform a second clean to dataset
Remove values from the first essay.
2.4.1 Plot observed reduced data as a scatterplot
2.5 Generate reduced model
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's method ['lmerModLmerTest']
## Formula: average ~ day:code:clone + (1 | day:code:clone)
## Data: dataset_clean2
##
## AIC BIC logLik deviance df.resid
## 7362.9 7534.5 -3647.5 7294.9 1116
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -7.6634 -0.4505 0.0445 0.4939 4.3671
##
## Random effects:
## Groups Name Variance Std.Dev.
## day:code:clone (Intercept) 3.196 1.788
## Residual 30.859 5.555
## Number of obs: 1150, groups: day:code:clone, 155
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 10.8521 0.5149 149.1406 21.074 < 2e-16 ***
## day:codeP. palmivora | 1102:cloneCCN51 14.8449 0.3847 141.8160 38.592 < 2e-16 ***
## day:codeP. palmivora | 1158:cloneCCN51 14.7646 0.3847 141.8160 38.384 < 2e-16 ***
## day:codeP. palmivora | 906:cloneCCN51 -0.4640 0.5986 653.4711 -0.775 0.438588
## day:codeP. palmivora | 920:cloneCCN51 7.5864 0.3975 161.6772 19.087 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:cloneCCN51 17.3753 0.3847 141.8160 45.171 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:cloneCCN51 16.2173 0.3847 141.8160 42.160 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:cloneCCN51 16.0670 0.3847 141.8160 41.770 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:cloneCCN51 16.1097 0.3847 141.8160 41.881 < 2e-16 ***
## day:codeP. palmivora | 1102:cloneCepec_2004 13.6108 0.3847 141.8160 35.384 < 2e-16 ***
## day:codeP. palmivora | 1158:cloneCepec_2004 12.7353 0.3847 141.8160 33.108 < 2e-16 ***
## day:codeP. palmivora | 920:cloneCepec_2004 4.8855 0.3847 141.8160 12.701 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:cloneCepec_2004 16.2081 0.3847 141.8160 42.136 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:cloneCepec_2004 16.2956 0.3847 141.8160 42.364 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:cloneCepec_2004 16.6957 0.3847 141.8160 43.404 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:cloneCepec_2004 16.1155 0.3847 141.8160 41.896 < 2e-16 ***
## day:codeP. palmivora | 1102:cloneCP49 15.2151 0.3847 141.8160 39.555 < 2e-16 ***
## day:codeP. palmivora | 1158:cloneCP49 15.8389 0.3847 141.8160 41.177 < 2e-16 ***
## day:codeP. palmivora | 906:cloneCP49 -0.6561 0.4670 299.9738 -1.405 0.161077
## day:codeP. palmivora | 920:cloneCP49 5.7741 0.3975 161.6772 14.527 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:cloneCP49 18.0267 0.3847 141.8160 46.864 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:cloneCP49 17.5476 0.3847 141.8160 45.619 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:cloneCP49 18.3890 0.3847 141.8160 47.806 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:cloneCP49 18.4667 0.3847 141.8160 48.008 < 2e-16 ***
## day:codeP. palmivora | 1102:clonePS1319 15.8531 0.3847 141.8160 41.214 < 2e-16 ***
## day:codeP. palmivora | 1158:clonePS1319 15.4167 0.3847 141.8160 40.079 < 2e-16 ***
## day:codeP. palmivora | 906:clonePS1319 2.3426 0.5986 653.4711 3.913 0.000101 ***
## day:codeP. palmivora | 920:clonePS1319 7.0675 0.3847 141.8160 18.374 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1091:clonePS1319 16.7054 0.3847 141.8160 43.429 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1151:clonePS1319 16.2934 0.3847 141.8160 42.358 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1205:clonePS1319 17.3136 0.3847 141.8160 45.010 < 2e-16 ***
## day:codeP. theobromicola sp. nov. | 1285:clonePS1319 16.5566 0.3847 141.8160 43.043 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Correlation matrix not shown by default, as p = 32 > 12.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient2.5.1 Plot final model adjust
2.5.2 Test significance of fixed effects
2.5.3 Test significance of random effects
2.5.4 Plot a residual histogram
2.6 Plot observed vs predicted with reduced data as a scatterplot
2.6.1 Generate pairwise comparisons
2.6.2 Include alpha-numeric indicators of comparisons significance
## code clone day lsmean SE df lower.CL upper.CL .group
## P. palmivora | 906 CP49 3 8.88 1.45 315 6.03 11.7 A
## P. palmivora | 906 CCN51 3 9.46 1.84 612 5.85 13.1 A
## P. palmivora | 906 PS1319 3 17.88 1.84 612 14.27 21.5 AB
## P. palmivora | 920 Cepec_2004 3 25.51 1.22 184 23.11 27.9 BC
## P. palmivora | 920 CP49 3 28.17 1.25 201 25.70 30.6 CD
## P. palmivora | 920 PS1319 3 32.05 1.22 184 29.65 34.5 CD
## P. palmivora | 920 CCN51 3 33.61 1.25 201 31.14 36.1 D
## P. palmivora | 1158 Cepec_2004 3 49.06 1.22 184 46.66 51.5 E
## P. palmivora | 1102 Cepec_2004 3 51.68 1.22 184 49.28 54.1 EF
## P. palmivora | 1158 CCN51 3 55.15 1.22 184 52.75 57.5 EFG
## P. palmivora | 1102 CCN51 3 55.39 1.22 184 52.99 57.8 EFG
## P. palmivora | 1102 CP49 3 56.50 1.22 184 54.10 58.9 FGH
## P. palmivora | 1158 PS1319 3 57.10 1.22 184 54.70 59.5 FGH
## P. palmivora | 1158 CP49 3 58.37 1.22 184 55.97 60.8 FGHI
## P. palmivora | 1102 PS1319 3 58.41 1.22 184 56.01 60.8 FGHI
## P. theobromicola sp. nov. | 1205 CCN51 3 59.05 1.22 184 56.65 61.5 GHIJ
## P. theobromicola sp. nov. | 1285 CCN51 3 59.18 1.22 184 56.78 61.6 GHIJ
## P. theobromicola sp. nov. | 1285 Cepec_2004 3 59.20 1.22 184 56.80 61.6 GHIJ
## P. theobromicola sp. nov. | 1091 Cepec_2004 3 59.48 1.22 184 57.08 61.9 GHIJ
## P. theobromicola sp. nov. | 1151 CCN51 3 59.50 1.22 184 57.10 61.9 GHIJ
## P. theobromicola sp. nov. | 1151 PS1319 3 59.73 1.22 184 57.33 62.1 GHIJ
## P. theobromicola sp. nov. | 1151 Cepec_2004 3 59.74 1.22 184 57.34 62.1 GHIJ
## P. theobromicola sp. nov. | 1285 PS1319 3 60.52 1.22 184 58.12 62.9 GHIJ
## P. theobromicola sp. nov. | 1205 Cepec_2004 3 60.94 1.22 184 58.54 63.3 GHIJ
## P. theobromicola sp. nov. | 1091 PS1319 3 60.97 1.22 184 58.57 63.4 GHIJ
## P. theobromicola sp. nov. | 1205 PS1319 3 62.79 1.22 184 60.39 65.2 HIJ
## P. theobromicola sp. nov. | 1091 CCN51 3 62.98 1.22 184 60.58 65.4 HIJ
## P. theobromicola sp. nov. | 1151 CP49 3 63.49 1.22 184 61.10 65.9 HIJ
## P. theobromicola sp. nov. | 1091 CP49 3 64.93 1.22 184 62.53 67.3 IJ
## P. theobromicola sp. nov. | 1205 CP49 3 66.02 1.22 184 63.62 68.4 J
## P. theobromicola sp. nov. | 1285 CP49 3 66.25 1.22 184 63.85 68.7 J
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## P value adjustment: tukey method for comparing a family of 31 estimates
## significance level used: alpha = 0.012.6.3 Plot multiplicity comparisons
2.6.4 Plot estimates
